## [1] "O77_p4_con_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
68,437,598 |
68,437,598 |
| Not Truncated |
38,537,742 |
40,669,996 |
| Truncated |
29,899,856 |
27,767,602 |
Truncated Read Length
| Average Length Truncated |
47.4 |
47 |
Mapping Efficiency
| Too Short To Map |
4,568,809 |
4,822,896 |
| Unique Alignments |
58,424,592 |
56,921,482 |
| Multiple Alignments |
2,500,650 |
2,588,830 |
| Failed To Align |
2,943,547 |
4,104,390 |
| Paired |
49,035,064 |
49,035,064 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
25,041,457 |
| Invalid Pairs |
23,993,607 |
| Same Circularised |
30,005 |
| Same Dangling Ends |
3,907,025 |
| Same Fragment Internal |
10,936,094 |
| Re Ligation |
6,639,247 |
| Contiguous Sequence |
270,646 |
| Wrong Size |
2,210,590 |
| Total Pairs |
49,035,064 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
25,041,457 |
35,040 |
| Cis-close (<10Kbp) |
2,000,586 |
3,044 |
| Cis-far (>10Kbp) |
14,782,729 |
18,375 |
| Trans |
8,258,142 |
13,621 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
